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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGTCAGGAGTTGCTATGACGAGGGTAAGCGTGTCGCAGAAACACTGATGTTTGACTATCACAGGCAGCATGGCATTGgtaatatttttagttcatacctttttgtcttgtgatgtactggattgtagttctccttaataagtattttccaatctatctctgtag

Basic information

species Oryza sativa
transcript LOC_Os03g16980.5
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g16980.5 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G044027_T02 (Zea mays), 5'ss of exon 8
GAGTCAGGAGTTGCTATGACGAGGGTAAGCGTGTCGCAGAAACACTGATGTTTGACTATCACAGGCAGCATGGCATTGgtaatattt-----------------------ttagttcata--cctttttgtcttgtgatg--tactggattgtagttctccttaataagtattttccaatctatctctgtag
|||||||||| || ||||| |||||||||||||| ||||| || |||||||| ||||||||||||||||||||||||||||||| ||                       |||| |||||  ||| ||| |  ||||||   |   || || |  ||   | | |  | |||||   ||||||| |||||||
GAGTCAGGAGCTGTTATGATGAGGGTAAGCGTGTAGCAGAGACGCTGATGTTCGACTATCACAGGCAGCATGGCATTGgtaatacttcatcttgcacttaaactgtaatattagctcatagccctctttattgtgtgataactctaggcttatgatttgtcctcagcaatatttat-aatctatgtctgtag

upper sequence: LOC_Os03g16980.5 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G157772_T01 (Zea mays), 5'ss of exon 5
-GAGTCAGGAGTTGCTATGACGAGGGTAAGCGTGTCGCA-GAAACACTGATGTTTGACTATCACAGGCAGCATGGCATTGgtaatatttt--------------------------tagttcatacctttttgtcttgtgatgta---ctgga-ttgtagttctcct-taataagtattttccaatctatctctgtag
    | |||||||| ||||| |||||||||||||| ||| || ||  ||||||| ||||||||||||||||||||||||||||| | ||                           ||| ||||| |  | | | || |||  ||   ||||  || |  || |  | | |  |||||||  || ||||| |||||||
GTGTTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCAAGAGACGTTGATGTTCGACTATCACAGGCAGCATGGCATTGgtaacacttcatctttcacttaaacttcaatattagtagctcatagccctctttgttatgagataactctgggcttatgatttttttcttaacagtatttatca-tctatgtctgtag

upper sequence: LOC_Os03g16980.5 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G177373_T02 (Zea mays), 5'ss of exon 8
GAGTCAGGAGTTGCTATGACGAGGGTAAGCGTGTCGCAGAAACACTGATGTTTGACTATCACAGGCAGCATGGCATTGgtaatatttt--------------------------tagttcata--cctttttgtcttgtgatg-tactggattgtagttctccttaataa--gtattttccaatctatctctgtag
| || |||||||| ||||| |||||||||||||| ||||| |   ||||||||||||||||||||||||||||||||||||| | ||                           ||| |||||  ||| |||||  ||||||    ||||  |   | | |  ||  |||  ||||||  || ||||| |||||||
GTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCAGAGATGTTGATGTTTGACTATCACAGGCAGCATGGCATTGgtaacacttcatctttcacttaaacttcaatattagtagctcatagccctctttgttatgtgataactctgggcttatgatttttttcttaacggtatttatca-tctatgtctgtag

upper sequence: LOC_Os03g16980.5 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G165357_T02 (Zea mays), 5'ss of exon 7
GAGTCAGGAGTTGCTATGACGAGGGTAAGCGTGTCGCAGAAACACTGATGTTTGACTATCACAGGCAGCATGGCATTGgtaatatttt--------------------------tagttcata--cctttttgtcttgtgatg--tactggattgtagttctccttaataagtattttccaatctatctctgtag
| || |||||||| ||||| |||||||||||||| ||||| || |||||||| ||||||||||||||||||||||||||||| | ||                           ||| |||||  ||| |||||  ||||||   |   || || |  || |   | |  |||||||  || ||||| |||||||
GTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCAGAGACGCTGATGTTCGACTATCACAGGCAGCATGGCATTGgtaacacttcatctttcacttaaacttcaatattagtagctcatagccctctttgttatgtgataactctgggcttatgattttttattaacagtatttatca-tctatgtctgtag

upper sequence: LOC_Os03g16980.5 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G382038_T01 (Zea mays), 5'ss of exon 9
GAGTCAGGAGTTGCTATGACGAGGGTAAGCGTGTCGCAGAAACACTGATGTTTGACTATCACAGGCAGCATGGCATTGgtaatatttt--------------------------tagttcata--cctttttgtcttgtgatg--tactggattgtagttctccttaata-agtattttccaatctatctctgtag
| || |||||||| ||||| |||||||||||||| ||||| |   ||||||||||||||||||||||||||||||||||||| | ||                           ||| |||||  ||| |||||  ||||||   |   || || |  || |  |    | |||||||  || ||||| |||||||
GTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCAGAGATGTTGATGTTTGACTATCACAGGCAGCATGGCATTGgtaacacttcatctttcacttaaacttcaatattagtagctcatagccctctttgttatgtgataactctgggcttatgatttttttcttgacagtatttatca-tctatgtctgtag

upper sequence: LOC_Os03g16980.5 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G300412_T01 (Zea mays), 5'ss of exon 14
GAGTCAGGAGTTGCTATGACGAGGGTAAGCGTGTCGCAGAAACACTGATGTTTGACTATCACAGGCAGCATGGCATTGgtaatatttt--------------------------tagttcata--cctttttgtcttgtgatg--tactggattgtagttctccttaataagtat-tttccaatctatctctgtag
| || |||||||| ||||| |||||||||||||| || || ||  |||||||||||||||||| |||||||||||||||||| | ||                           ||| |||||  ||| |||||  ||||||   |   || || |  || |  ||  |||   | |||   |||||| |||||||
GTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCTGAGACGTTGATGTTTGACTATCACAAGCAGCATGGCATTGgtaacacttcatctttcacttaaacttcaatattagtagctcatagtcctctttgttatgtgataactctgggcttatgattttttttcttaacagtgtttatcatctatgtctgtag

upper sequence: LOC_Os03g16980.5 (Oryza sativa), 5'ss of exon 8
lower sequence: GLYMA12G06990.1 (Glycine max), 5'ss of exon 8
GAGTCAGGAGTTGCTATGACGAGGGTAAGCGTGTCGCAGAAACACTGATGTTTGACTATCACAGGCAGCATGGCATTGgtaatatttttagttcatacctttttgtcttgtgatgtactggattgtagttctccttaataagtattttccaatctatctctgtag--------------------------
||||  | ||||||||||| ||||| || ||||| || |||||  |||||||||| ||||| ||||||||||| || |||||| | ||   ||| |   ||| |   | ||  | |  ||  |  | ||| |   |  ||   ||||| |  | ||  |     |                          
GAGTTCGTAGTTGCTATGATGAGGGGAAACGTGTGGCTGAAACTTTGATGTTTGATTATCATAGGCAGCATGGAATAGgtaatttcttctcttctt--ttttcttcatagttgtctgttgc-tccttgttataactggtagaaatttttctctgtaatttaactgagttttctatatttctttcaacatag

upper sequence: LOC_Os03g16980.5 (Oryza sativa), 5'ss of exon 8
lower sequence: GLYMA11G15010.1 (Glycine max), 5'ss of exon 8
GAGTCAGGAGTTGCTATGACGAGGGTAAGCGTGTCGCAGAAACACTGATGTTTGACTATCACAGGCAGCATGGCATTGgtaat-----atttttagttcatacctttttgtcttgtgatgtactg--gattgtagttctccttaataagtattttccaatctatctctgtag----------------------------------------------
||||  ||||||| ||||| ||||| |||||||| ||||||||  |||||||||| ||||| ||||||||||| || ||||||     || |||| ||  | | ||| |   | |  |  |      |||||  |        | ||    |||| || |     |   ||                                               
GAGTTCGGAGTTGTTATGATGAGGGCAAGCGTGTTGCAGAAACTTTGATGTTTGATTATCATAGGCAGCATGGAATCGgtaattccttatctttattttttccttttctccttggcaacatctcattgattgagggcacaaacagtacacgttttgcactgctgttaactaataagcaataactcaatgtgatgcttattttcatatttttctctcag

upper sequence: LOC_Os03g16980.5 (Oryza sativa), 5'ss of exon 8
lower sequence: GLYMA15G04500.2 (Glycine max), 5'ss of exon 9
GAGTCAGGAGTTGCTATGACGAGGGTAAGCGTGTCGCAGAAACACTGATGTTTGACTATCACAGGCAGCATGGCATTGgtaat-----atttttagttc------atacctttttgtcttgt----gatgtactggattgtagttctccttaataagt--attttccaatctatctctgtag-------------
||||  | ||||||||||| ||||| || || || || || ||| |||||||||| || || ||||||||||| |||||||||      | |||  |||      ||  ||| | || ||||    |   ||    || |   || | |||  |   |  | |     |  | | | | ||              
GAGTTCGTAGTTGCTATGATGAGGGGAAACGGGTGGCTGAGACATTGATGTTTGATTACCATAGGCAGCATGGAATTGgtaatttattgtctttttttccttataatttcttctcgttttgtttaaggcatatccaatagagatttttctttgttttttaactccttgaggtgtttatatatcctttcaacatag

upper sequence: LOC_Os03g16980.5 (Oryza sativa), 5'ss of exon 8
lower sequence: GLYMA13G40960.1 (Glycine max), 5'ss of exon 9
GAGTCAGGAGTTGCTATGACGAGGGTAAGCGTGTCGCAGAAACACTGATGTTTGACTATCACAGGCAGCATGGCATTGgtaatatttttagttcatacctttttgtcttgtgatgtactggattgtagttctcc--ttaataagtattttccaatcta---tctctgtag------------------------
||||  | ||||||||||| ||||| || || || || || ||| |||||||||| || || ||||||||||| ||||||||| | ||   ||| |  | || |   || |  |    | | ||  |  | |||  |  | |  ||| ||    |||    ||  ||| |                        
GAGTTCGTAGTTGCTATGATGAGGGGAAACGGGTGGCCGAGACATTGATGTTTGATTACCATAGGCAGCATGGGATTGgtaatttcttgtcttcttttccttgtaatttcttctcattttgtttacacatatccagtagagatttatctttgtttcttaactccttgtggtgtttatgtctcctttcaacatag

upper sequence: LOC_Os03g16980.5 (Oryza sativa), 5'ss of exon 8
lower sequence: GLYMA11G15020.1 (Glycine max), 5'ss of exon 8
GAGTCAGGAGTTGCTATGACGAGGGTAAGCGTGTCGCAGAAACACTGATGTTTGACTATCACAGGCAGCATGGCATTGgtaatatttttagttcatacctttttgtcttgtgatgtactggattgtagttctccttaataagtattttccaatctatctctgtag----------------------------------------------------------
||||  | ||||||||||| ||||| || ||||| || |||||  |||||||||| ||||| ||||||||||| || |||||| | |    ||| |  |||  |   ||||  |  | ||  |||| ||| || || |||  | | ||    ||  | | | |||                                                          
GAGTTCGTAGTTGCTATGATGAGGGGAAACGTGTGGCTGAAACTTTGATGTTTGATTATCATAGGCAGCATGGAATAGgtaatttctgctcttcttttcttcatag-ttgttgttgattg--ttgttgttttc-ttcatagttgtcttttgttccttgt-tatagctggtagaaaattttcttttgtaagttaactgagttttttatatttctttcaacatag

upper sequence: LOC_Os03g16980.5 (Oryza sativa), 5'ss of exon 8
lower sequence: AT5G59290.2 (Arabidopsis thaliana), 5'ss of exon 7
GAGTCAGGAGTTGCTATGACGAGGGTAAGCGTGTCGCAGAAACACTGATGTTTGACTATCACAGGCAGCATGGCATTGgtaatatttttagttcat--acctttttgtcttgtgatgtactggatt--gtagttctcctta-ataagtattttccaatctatc-tctgtag
| ||  |||||||||||||||| || ||||| || || |||||  ||||||||||||| ||||| || |||||||||||| |  ||| || |||    | ||   ||  |     | | ||  ||   ||  |||   | | ||    |||  ||  | | || | |||||
GGGTTCGGAGTTGCTATGACGAAGGCAAGCGGGTAGCCGAAACCTTGATGTTTGACTACCACAGACAACATGGCATTGgtcagttttctacttccctaaactcactgcatcacttttttctttatccagtgattcctttaagattctcattggcctgtttgtcatttgtag

upper sequence: LOC_Os03g16980.5 (Oryza sativa), 5'ss of exon 8
lower sequence: AT3G46440.1 (Arabidopsis thaliana), 5'ss of exon 7
GAGTCAGGAGTTGCTATGACGAGGGTAAGCGTGTCGCAGAAACACTGATGTTTGACTATCACAGGCAGCATGGCATTGgtaa----tattttt---agttcatacct----ttttgtcttgtgatgtac-----tggattgtagttctccttaat-----aagtattttccaatctatctctgtag
| || ||||| || ||||| || || |||||||| || || ||  ||||||||||||| |||||||| ||||| ||||||||     |||||     | ||   | |    |||   | ||| || | |        ||| |  || ||||| ||     || |  |||    |   ||| |||||
GTGTTAGGAGCTGTTATGATGAAGGCAAGCGTGTTGCTGAGACCTTGATGTTTGACTACCACAGGCAACATGGAATTGgtaagttgcattttctcaggctctcgcttcaactttctccctgtaatttgcatcaacatattctcattgtcctttattccttaaattgtttttgtttcttctttgtag

upper sequence: LOC_Os03g16980.5 (Oryza sativa), 5'ss of exon 8
lower sequence: Vv13s0019g00840.t01 (Vitis vinifera), 5'ss of exon 8
GAGTCAGGAGTTGCTATGACGAGGGTAAGCGTGTCGCAGAAACACTGATGTTTGACTATCACAGGCAGCATGGCATTGgtaatatttttagttcatacctttttgtcttgtgatgtactggattgtagttctccttaataagtattttccaatctatctctgtag------------------------------------------------------------------------------------------------------
||||||||||||||||||| ||||| ||||| || || ||||| ||||||||||| ||||||||||||||||| || ||||| |||    | ||   |  | |  ||     |   |    |  |     | |     ||   |  ||| | ||  || |||  |                                                                                                      
GAGTCAGGAGTTGCTATGATGAGGGAAAGCGAGTGGCTGAAACTCTGATGTTTGATTATCACAGGCAGCATGGAATAGgtaaaattg--ggctccctctctctgatccatacacccaacacacagacacccccacacctacacacattc-actcagtcactgatgggatgtgtaaaattgttcactcccttcccctccctctctctatctgaaactctactttccaatgcactctcactttattttgaaatggtgatcctataacag

upper sequence: LOC_Os03g16980.5 (Oryza sativa), 5'ss of exon 8
lower sequence: PP1S189_118V6.1 (Physcomitrella patens), 5'ss of exon 8
GAGTCAGGAGTTGCTATGACGAGGGTAAGCGTGTCGCAGAAACACTGATGTTTGACTATCACAGGCAGCATGGCATTGgta---atatttttagt-tcatacctttt-tgtcttgtgatgtactg-gattgtagttctccttaataagtattttccaatctatctctgtag-------
|||| || || |||||||||||||| |||||||| || || || || ||||||||||| || |||||||||||| ||||||   | |||  | || |  || ||||| |   ||   | |  ||  | || ||  ||     |||  ||| |         |  | | ||        
GAGTAAGAAGCTGCTATGACGAGGGAAAGCGTGTTGCTGAGACTCTTATGTTTGACTACCATAGGCAGCATGGCGTTGgtatatacattcctcgtgttgtatcttttctaagttaacacgctctacgcttttatgtcggtccaatgtgtactagaagcgtaaaatatttaaacctggc

upper sequence: LOC_Os03g16980.5 (Oryza sativa), 5'ss of exon 8
lower sequence: EFJ17446 (Selaginella moellendorffii), 5'ss of exon 7
GAGTCAGGAGTTGCTATGACGAGGGTAAGCGTGTCGCAGAAACACTGATGTTTGACTATCACAGGCAGCATGGCATTGgtaatatttttagttcatacctttttgtcttgtgatgtactggattgtagttctccttaataagtattttccaatctatctctgtag
| || ||||| ||||| |||||||| || || || || |||||  ||||||||||||||||||||||||| || ||||||    |   | | |  || |||  || |    | | |   |    ||| |||||                                
GTGTTAGGAGCTGCTACGACGAGGGAAAACGCGTGGCCGAAACGTTGATGTTTGACTATCACAGGCAGCACGGGATTGgtttgctcgattgctt-tagcttgatgacgctggttctgacgtccagtaattctcag------------------------------

upper sequence: LOC_Os03g16980.5 (Oryza sativa), 5'ss of exon 8
lower sequence: EFJ35029 (Selaginella moellendorffii), 5'ss of exon 7
GAGTCAGGAGTTGCTATGACGAGGGTAAGCGTGTCGCAGAAACACTGATGTTTGACTATCACAGGCAGCATGGCATTGgtaatatttttagttcatacctttttgtcttgtgatgtactggattgtagttctccttaataagtattttccaatctatctctgtag
| || ||||| ||||| |||||||| || || || || |||||  ||||||||||||||||||||||||| || ||||||    |   | | |  || |||  || |    | | |   |    ||| |||||                                
GTGTTAGGAGCTGCTACGACGAGGGAAAACGCGTGGCCGAAACGTTGATGTTTGACTATCACAGGCAGCACGGGATTGgtgtgctcgattgctt-tagcttgatgacgctggttctgacgtccagtaattctcag------------------------------

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|58590735|gb|CF989043.1|CF989043
EST:     GCGTGTCGCAGAAACACTGATGTTTGACTATCACAGGCAGCATGGCATTG                         AGATCCGAATTGCCAGGATTTTCAACACCTATGGACCTAGGATGAACATTG
genomic: GCGTGTCGCAGAAACACTGATGTTTGACTATCACAGGCAGCATGGCATTGgtaatatttt ... atctctgtagAGATCCGAATTGCCAGGATTTTCAACACCTATGGACCTAGGATGAACATTG
EST: gi|30229035|gb|CB966926.1|CB966926
EST:     GCGTGTCGCAGAAACACTGATGTTTGACTATCACAGGCAGCATGGCATTG                         AGATCCGATTTGC-AGGATTT-CAACAC-TATGGACCTAGGATGAACCTTG
genomic: GCGTGTCGCAGAAACACTGATGTTTGACTATCACAGGCAGCATGGCATTGgtaatatttt ... atctctgtagAGATCCGAATTGCCAGGATTTTCAACACCTATGGACCTAGGATGAACATTG
EST: gi|313080404|gb|HO213412.1|HO213412
EST:     GCGTGTCGCAGAAACACTGATGTTTGACTATCACAGGCAGCATGGCATTG                         AGATCCGAATTGCCAGGATTTTCAACACCTATGGACCTAGGATGAACATTG
genomic: GCGTGTCGCAGAAACACTGATGTTTGACTATCACAGGCAGCATGGCATTGgtaatatttt ... atctctgtagAGATCCGAATTGCCAGGATTTTCAACACCTATGGACCTAGGATGAACATTG
EST: gi|33380802|gb|CF196145.1|CF196145
EST:     GCGTGTCGCAGAAACACTGATGTTTGACTATCACAGGCAGCATGGCATTG                         AGATCCGAATTGCCAGGATTTTCAACACCTATGGACNNNNNATGAACATTG
genomic: GCGTGTCGCAGAAACACTGATGTTTGACTATCACAGGCAGCATGGCATTGgtaatatttt ... atctctgtagAGATCCGAATTGCCAGGATTTTCAACACCTATGGACCTAGGATGAACATTG
EST: gi|58656016|gb|CK044696.1|CK044696
EST:     GCGTGTCGCAGAAACACTGATGTTTGACTATCACAGGCAGCATGGCATTG                         AGATCCGAATTGCCAGGATTTTCAACACCTATGGACCTAGGATGAACATTG
genomic: GCGTGTCGCAGAAACACTGATGTTTGACTATCACAGGCAGCATGGCATTGgtaatatttt ... atctctgtagAGATCCGAATTGCCAGGATTTTCAACACCTATGGACCTAGGATGAACATTG
EST: gi|58672962|gb|CK061648.1|CK061648
EST:     GCGTGTCGCAGAAACACTGATGTTTGACTATCACAGGCAGCATGGCATTG                         AGATCCGAATTGCCAGGATTTTCAACACCTATGGACCTAGGATGAACATTG
genomic: GCGTGTCGCAGAAACACTGATGTTTGACTATCACAGGCAGCATGGCATTGgtaatatttt ... atctctgtagAGATCCGAATTGCCAGGATTTTCAACACCTATGGACCTAGGATGAACATTG
EST: gi|58659773|gb|CK048453.1|CK048453
EST:     GCGTGTCGCAGAAACACTGATGTTTGACTATCACAGGCAGCATGGCATTG                         AGATCCGAATTGCCAGGATTTTCAACACCTATTGACCTAGGATGAACATTG
genomic: GCGTGTCGCAGAAACACTGATGTTTGACTATCACAGGCAGCATGGCATTGgtaatatttt ... atctctgtagAGATCCGAATTGCCAGGATTTTCAACACCTATGGACCTAGGATGAACATTG